Well unless or until you have space anomalyies other than black holes the easiest thing would be to have the black hole show once you lose a ship into one. I would assume a ship or probe could get at least a message off once it sees said black hole.

I noticed that they dont show up unless you have ran into it and have hyperspace physics researched. So unless there is another reason just take the hyperspace physics requirement off for them being displayed once they are run into.